Binding of ligands to enzyme

It has been adequately established that 3D structural information(s) with respect to a probable and potential therapeutic target in no way serves as a guarantee for the precise identification of the site of action of the substrate, or inhibitor, till such time when one lays ones hands onto a definite relevant complex ultimately. In actual practice, various conformational changes invariably come into being in the course of realistic binding of ligands to enzymes which are eventually not registered in the 3D structure of the enzyme critically. 

It is important to note, and should always be remembered, that all the rate and binding equations for cooperative and allosteric enzymes were derived under rapid equilibrium assumption. Therefore, all kinetic models for the cooperative phenomena can be equally well applied to enzyme reactions that are in the rapid equilibrium and to the binding of ligands to enzymes and proteins. 

Proteins, 109,110, 116.Seealso Enzymes Macromolecules average thermal amplitudes, MD simulations, 119 binding of ligands to, 120 dielectric relaxation time of, 122 electrostatic energies in, 122, 123-125 flexibility of, 209,221,226-227, 227 folding, 109,227... 

I would like to remind the audience that Mildred Cohn had shown that in some phosphotransferases the binding of ligands to the active site of the enzyme leads to an exclusion of water molecules in the neighborhood of manganese as part of the active site function. 

This is referred to as induced fit, a mechanism postulated by Daniel Koshland in 1958. Induced fit serves to bring specific functional groups on the enzyme into the proper position to catalyze the reaction. The conformational change also permits formation of additional weak bonding interactions in the transition state. In either case, the new enzyme conformation has enhanced catalytic properties. As we have seen, induced fit is a common feature of the reversible binding of ligands to proteins (Chapter 5). Induced fit is also important in the interaction of almost every enzyme with its substrate. 

Figure 8.1. A model of the transcriptional regulation of CYP3A expression by PXR. The PXR binds as a heterodimer with RXR to response elements in the promoter of CYP3A and other target genes. Binding of ligand to the PXR results in increased CYP3A enzyme activity, which in turn increases the hydroxylation of substrates such as steroids, bile acids, and drugs,...

Such transformations constitute the basis of thermodynamic cycles, which have been used extensively for evaluating the free energy of binding of ligands to an enzyme, hydration free energies of small molecules, enzymatic reactions, etc. 

A reaction between an enzyme, E, and substrate, S, to give a product, P, starts with binding of substrate to enzyme to form a complex, E S. This is similar to the interaction of ligand and receptor, L + R = L R, that we encountered before. The strength of this complex, expressed by an equilibrium constant, and the rate of conversion of E S into product, expressed by a kinetic constant, are two major parameters used to describe kinetic properties of an enzyme. The mathematical formalism used for enzyme kinetics today has been developed by North American chemists Leonor Michaelis and Maud Menten and subsequent authors and it is habitually called MM kinetics. 

The reaction starts with the binding of ATP to the H -liganded form of the enzyme, 2H Ei. In the presence of K, this binding is to the K -liganded enzyme form, 2K Ei or 2K E2, or to an occluded form between these two forms. The existence of such an occluded form has not yet been demonstrated, but its detection with filtration or column techniques similar to those used previously to measure occluded transported cations for Na,K-ATPase [113] will be very difficult, because of the rapid dissociation of from the enzyme [96]. Subsequent binding of Mg to 2H E] then leads to phosphorylation at an aspartyl residue [46,114]. The major phosphoenzyme then formed is a K -sensitive intermediate (2H E2-P), whereas a minor part (20%) exists as an ADP-sensitive intermediate (2H Ei-P) [92,93]. With... 

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